Posts Tagged 'Phylogenetics'

Is ‘the Drosophila‘ actually Drosophila?

This post was chosen as an Editor's Selection for ResearchBlogging.orgCelebrities commonly change their names on the path to stardom. Elton John began life as Reginald Kenneth Dwight, John Denver as Henry Deutschendorf, Jr, and Bela Lugosi as Be’la Ferenc Dezso Blasko. A name change can make someone more marketable in the fickle entertainment industry. However, once someone makes it big, their name usually stays the same (excepting P-Diddy and Prince, whose constant name changes became marketing strategies in themselves). A celebrity’s name becomes the branding that represents and sells their fame.

What about name changes for scientific celebrities? I’m not talking about people, but rather the components of nature that we observe around ourselves and adorn with nomenclature. There was (unnecessary) public uproar when Pluto was re-designated as a Kuiper Belt planetoid. Neil deGrasse Tyson even got hate mail from children when the American Museum of Natural History updated its displays accordingly. The change was the result of a non-unanimous scientific consensus attempting to better define the bodies of the solar system, but many people had become attached to the idea of PLANET Pluto and reacted negatively to the news.

Now a new conundrum is brewing within scientific circles as biologists try to decide what to do when the nomenclature describing a celebrity organism no longer jives with scientific observation. Nature News asks, ‘What’s in a name?’. Well, when the name is Drosophila melanogaster, there’s 100 years of glorious scientific discoveries in a name.

Photo by mr.checker

D. melanogaster, the common fruit fly, was a major workhorse behind the early 20th century genetic revolution. Researchers like Thomas Hunt Morgan harnessed the fly’s fast reproductive cycle and simple care requirements to elucidate the fundamentals of heredity. Since then, the powerful D. melanogaster model has exploded to become a principle contributer to research in genetics, neurology, development, biomechanics, and evolution. Found in almost any biology department around the world, this animal is of tremendous historical and contemporary importance to science; a true celebrity.

However, there is one slight problem; Drosophila melanogaster is probably not Drosophila melanogaster.

The issue here is the status of the genus, Drosophila. This genus, as it is currently recognized, contains 1,450 species of fruit flies. A genus, or any level of taxonomic organization, is supposed to be monophyletic, that is; composed only of species that are evolutionarily closer to one another than they are to the members of any other genus. However, with Drosophila, this has been shown through extensive molecular and morphological analysis not to be the case.

Fruit Fly supertree. Adapted from Van der Linde and Houle, 2008

Look at the phylogenetic tree to the left (for an overview of phylogenetics, read this post). Each node on the tree represents a group of species of the same genus. Notice, however, that the 1,450 species of the Drosophila genus are split up into six different clades, interspersed with other genera. This is called paraphyly, and it points out an error in the taxonomic nomenclature. All the species of a given genus should be grouped together, in a monophyletic relationship. Ultimately, this means that there is going to have to be some reorganization of the genus. Some members of Drosophila are going to be ousted and given new names.

The obvious solution to preserve the celebrated D. melanogaster species name would seem to be leaving its clade (marked with a red arrow) as genus Drosophila and renaming the others. However, there are two problems with this. First of all, restructuring the genus in the manner would push out, and require the renaming, of 1,100 species of fruit flies. Furthermore, the type species Drosophila funebris (marked with an orange arrow), the animal from which the Drosophila genus was originally described in 1787, lies in a different clade than D. melanogaster. A recent petition to re-designate the genus type species as D. melanogaster was voted down by the International Commission on Zoological Nomenclature.

As it looks at the moment, D. melanogaster is probably on its way to becoming Sophophora melanogaster. This has generated shock and disbelief from biologists; citing possible research impediments should the name change go through. In addition, they surely have a sentimental attachment to the name of their favorite laboratory arthropod. When biologists say ‘Drosophila‘, they mean Drosophila melanogaster. This celebrated animal has a strong claim to being the most important and powerful research tool biologists have in their arsenal. However, even D. melanogaster, like Pluto, may need to bend in name to the powers of parsimonious taxonomic nomenclature.
_____________________________________________________________________

Read more about the Drosophila name fight here and here at Nature News, or here at Catalogue of Organisms

Check out some of my other posts about phylogenetics:

References:

    Kim Van der Linde, & David Houle (2008). A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae)Insect Syst. Evol., 39, 241-267

Unraveling Arthropoda

This post was chosen as an Editor's Selection for ResearchBlogging.orgA new paper, published online in Nature this week, aims to resolve long-standing disputes within Arthropod phylogenetics. This work offers strong evidence for, and opens new, perplexing questions about, the deep evolutionary history of arthropods.

The phylum Arthropoda consists of four major subphyla:

  • Chelicerata – Arachnids, horseshoe crabs, sea spiders.
  • Myriapoda – Centipedes, millipedes.
  • Crustacea – Crabs, lobsters, shrimp, copepods, ostracods, barnacles, pill bugs, brine shrimp, water fleas, remipedes, ect.
  • Hexapoda – Insects, silverfish, springtails.

All known arthropods are included in these subphyla. However, the interrelation of the subphyla has long been in contention. Up to now, a series of morphological and molecular-based classification paradigms have been employed to parsimoniously resolve the deep phylogeny of arthropods; with mixed results. Two of the competing hypotheses of deep arthropod phylogenetics are the Paradoxopoda and Mandibulata models.

Both Mandibulata and Paradoxopoda propose a Pancrustacean clade consisting of Hexapods and Crustaceans as closely related sister groups. They differ in their treatment of the Myriapods and Chelicerates. Paradoxopoda has Myriapods and Chelicerates as closely related sister groups. Mandibulata, on the other hand, has Myriapods as a sister group to Pancrustaceans, and Chelicerates as a distant, early-branching clade of arthropods. While Mandibulata is supported by taxonomy (Crustaceans, Hexapods, and Myriapods all have mandibles, where as Chelicerates have chelicerae for mouthparts), Paradoxopoda is primarily supported by recent mitochondrial molecular pylogenetics.

Also under contention is the relationship between Crustaceans and Hexapods within the increasingly well supported Pancrustacean clade. It has not yet been settled if the two are distinct sister groups, or if the Hexapods are nested within the Crustaceans. If the latter is true, researchers have not been able to determine which branch of the Crustaceans gave rise to the Hexapods.

In the present study, researchers at University of Maryland, Duke, and the Natural History Museum of LA have dramatically improved on previous molecular approaches for inferring deep arthropod phylogenetics. They did this by increasing the number and diversity of arthropod species included, as well as the type and amount of genetic sequence characters used. Whereas previous approaches used mitochondrial genetic sequences, resulting in the morphologically perplexing Paradoxopoda model; the researchers in this study instead used nuclear protein-coding genes. Nuclear genes have been increasingly used to resolve deep evolutionary relationships in animals.

The researchers included in their molecular phylogenetic analysis 75 arthropod species. The 75 arthropod taxa were chosen to encompass the broadest spectrum of known arthropod groups. From each of these species, they sequenced 62 nuclear genes; totaling 41 thousand bases of DNA sequence per species. These sequence data sets from the 75 different arthropods were compared to one another, producing this phylogenetic tree:

Maximum likelihood phylogenetic tree of arthropods. Adapted from Regier et al., 2010.

This tree further supports a Pancrustacean clade consisting of Hexapods and Crustaceans. In addition, this work supports the Mandibulata model of deep evolutionary relationships within Arthropoda. Pancrustacea is sister to the Myriapods, forming the Mandibulata clade; which is then sister to the early-branching Chelicerates. This reconstruction strongly refutes the mitochondrial Paradoxopoda model.

The most notable results of this study are in regard to the internal structure of the Pancrustacean clade. Instead of a distinct separation between Crustaceans and Hexapods, we see four resolved clades within Pancrustacea. The Hexapod clade is upheld and nested completely within Crustacea. In addition Crustaceans are split into three paraphyletic clades; Vericrustacea, Oligostraca, and Xenocarida. Vericrustacea (‘true crustaceans’) includes the decapods (crabs and lobsters), mantis shrimp, barnacles, copepods, and branchiopods; most of the critters commonly thought of as crustaceans. Oligostraca is a strange and early branching crustacean group that includes ostracods, tongue worms, and branchiurans. Xenocarida (‘strange shrimps’) includes remipedes and cephalocarids.

It turns out that, according to this analysis, the Xenocarids are the long sought-after sister group to Hexapods. Together they form the new clade Miracrustacea (‘surprising crustacean’). The Miracrustaceans are sister to the Vericrustaceans, forming a clade that is in turn sister to the Oligostraca, rounding out Pancrustacea.

This study causes some serious upheavals in the Pancrustacean clade; breaking Crustaceans into three paraphyletic clades, placing remipedes as close sister taxa to Hexapods, and nesting the Hexapods completely within the Crustaceans. At the same time it presents new and exciting questions to morphologists and evolutionary-developmental biologists.

Further morphological, genetic, and evolutionary study is required in order to understand the full implications of these newly resolved arthropod relationships. However, this research represents a robust step forward towards unraveling Arthropoda.

References:

  • Regier, J., Shultz, J., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J., & Cunningham, C. (2010). Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences Nature DOI: 10.1038/nature08742

Introduction to phylogenetics

Disclaimer: This intro to phylogenetics is criminally over-simplistic. There are links to much more in depth articles at the bottom of the post. Also, this post is a work in progress, and I will refine it as time goes on.

Phylogenetics is the organization of organisms according to their evolutionary relationships. Evolutionary relatedness is determined by comparing large numbers of characteristics between multiple organisms. These characters can be morphological features, molecular sequences, behavior, or bio-geographical distributions. The more characters two species share, the closer together they are phylogenetically. Phylogenetic relatedness can be displayed using a phylogenetic tree. Let’s familiarize ourselves with a generic phylogenetic tree:

The crucial components of a phylogenetic tree are nodes, branches, leaves, and the root. Each leaf represents an organism. Each node, represents the common ancestor of all the organisms that branch out of it. The root represents the common ancestor of every organism on the tree. Evolutionary time is represented along the “x” axis of the tree. On this tree, the common ancestor (node) of organisms A and B is more recent than the common ancestor of A and C. Now lets work backwards and talk about how this tree could have been built.

Continue reading ‘Introduction to phylogenetics’


I have moved.
Arthropoda can now be found here.

Michael Bok is a graduate student studying the visual system of mantis shrimp.

Flickr Photos

Johanneksenkirkko with a firey sunset.

Frozen Gulf of Finland

20161225-IMG_1292.jpg

20161225-IMG_1282.jpg

20161225-IMG_1184.jpg

20161225-IMG_1175.jpg

20161224-IMG_1146.jpg

Nudibranch from Lizard Island

20161225-IMG_1294.jpg

Bringing in the catch

More Photos